RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.4fRccM/RM_3723711.FriDec60408092024 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1733486888 Database = /scratch/tmp/rModeler.4fRccM/GCA_964195625.1_mMyoMys1.hap2.1 - Sequences = 327 - Bases = 1943289057 - N50 = 109873438 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 215313864-230693355 | [ 3 ] 199934374-215313864 | [ ] 184554884-199934374 | [ ] 169175393-184554883 | [ ] 153795903-169175393 | [ ] 138416413-153795903 | [ ] 123036922-138416412 | [ ] 107657432-123036922 | [ 2 ] 92277942-107657432 | [ 3 ] 76898451-92277941 | [ 3 ] 61518961-76898451 | [ 3 ] 46139471-61518961 | [ 3 ] 30759980-46139470 | [ 1 ] 15380490-30759980 | [ 3 ] 1000-15380490 |************************************************** [ 306 ] Storage Throughput = excellent ( 1668.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036234 bp ( 40030634 non ambiguous ) - Num Contigs Represented = 58 - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:49 (hh:mm:ss) Elapsed Time Round Time: 00:11:22 (hh:mm:ss) Elapsed Time : 352 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13074 repeats masked totaling 2390703 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035835 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10034435 bp After Masking: 7219706 bp Masked: 28.05 % -- Input Database Coverage: 10035835 bp out of 1943289057 bp ( 0.52 % ) Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:52 (hh:mm:ss) Elapsed Time, 5877 HSPs Collected Number of families returned by RECON: 856 Round Time: 00:03:38 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43735 repeats masked totaling 8103373 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040321 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30036121 bp After Masking: 20498954 bp Masked: 31.75 % -- Input Database Coverage: 40076156 bp out of 1943289057 bp ( 2.06 % ) Sampling Time: 00:01:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:12:19 (hh:mm:ss) Elapsed Time, 26096 HSPs Collected Number of families returned by RECON: 2477 Round Time: 00:14:43 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 141249 repeats masked totaling 26399721 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015551 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 90003951 bp After Masking: 60412533 bp Masked: 32.88 % -- Input Database Coverage: 130091707 bp out of 1943289057 bp ( 6.69 % ) Sampling Time: 00:05:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:10:55 (hh:mm:ss) Elapsed Time, 113332 HSPs Collected Number of families returned by RECON: 8748 Round Time: 01:18:37 (hh:mm:ss) Elapsed Time : 221 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 465429 repeats masked totaling 86877910 bp(s). - TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046563 bp Num Contigs Represented = 131 Non ambiguous bp: Initial: 270005024 bp After Masking: 172913772 bp Masked: 35.96 % -- Input Database Coverage: 400138270 bp out of 1943289057 bp ( 20.59 % ) Sampling Time: 00:17:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22967253 Comparison Time: 08:21:32 (hh:mm:ss) Elapsed Time, 347732 HSPs Collected Number of families returned by RECON: 36135 Round Time: 08:53:22 (hh:mm:ss) Elapsed Time : 519 families discovered. RepeatScout/RECON discovery complete: 1158 families found Classification Time: 00:24:34 (hh:mm:ss) Elapsed Time Program Time: 11:06:16 (hh:mm:ss) Elapsed Time